4yhk - Revision history

OCA at 10:55, 10 January 2024

OCA — Wed, 10 Jan 2024 10:55:12 GMT

←Older revision		Revision as of 10:55, 10 January 2024
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	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHK FirstGlance]. <br>		<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.21Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [https://pdbe.org/4yhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [https://www.ebi.ac.uk/pdbsum/4yhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhk ProSAT]</span></td></tr>		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [https://pdbe.org/4yhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [https://www.ebi.ac.uk/pdbsum/4yhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhk ProSAT]</span></td></tr>
	</table>		</table>

OCA at 08:14, 3 May 2023

OCA — Wed, 03 May 2023 08:14:30 GMT

←Older revision		Revision as of 08:14, 3 May 2023
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	<StructureSection load='4yhk' size='340' side='right'caption='[[4yhk]], [[Resolution\|resolution]] 2.21Å' scene=''>		<StructureSection load='4yhk' size='340' side='right'caption='[[4yhk]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4YHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4YHK FirstGlance]. <br>
-	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [~~http~~://pdbe.org/4yhk PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/4yhk PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhk ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [https://pdbe.org/4yhk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [https://www.ebi.ac.uk/pdbsum/4yhk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 20:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Nar, H]]	+	[[Category: Nar H]]
-	[[Category: Schiele, F]]	+	[[Category: Schiele F]]
-	~~[[Category: Antibody]]~~	+
-	~~[[Category: Antidote]]~~	+
-	~~[[Category: Dabigatran]]~~	+
-	~~[[Category: Immune system]]~~	+
-	~~[[Category: Pradaxa]]~~	+
-	~~[[Category: Reversal agent~~]]	+

OCA at 06:45, 12 June 2019

OCA — Wed, 12 Jun 2019 06:45:32 GMT

←Older revision		Revision as of 06:45, 12 June 2019
Line 1:		Line 1:
		+
	==Reversal Agent for Dabigatran==		==Reversal Agent for Dabigatran==
-	<StructureSection load='4yhk' size='340' side='right' caption='[[4yhk]], [[Resolution\|resolution]] 2.21Å' scene=''>	+	<StructureSection load='4yhk' size='340' side='right'caption='[[4yhk]], [[Resolution\|resolution]] 2.21Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHK FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHK FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [http://pdbe.org/4yhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [http://www.ebi.ac.uk/pdbsum/4yhk PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [http://pdbe.org/4yhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [http://www.ebi.ac.uk/pdbsum/4yhk PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=4yhk ProSAT]</span></td></tr>
	</table>		</table>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
Line 19:		Line 20:
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
		+	[[Category: Large Structures]]
	[[Category: Nar, H]]		[[Category: Nar, H]]
	[[Category: Schiele, F]]		[[Category: Schiele, F]]

OCA at 20:06, 13 January 2016

OCA — Wed, 13 Jan 2016 20:06:16 GMT

←Older revision		Revision as of 20:06, 13 January 2016
Line 1:		Line 1:
-	'''~~Unreleased~~ structure'''	+	==Reversal Agent for Dabigatran==
		+	<StructureSection load='4yhk' size='340' side='right' caption='[[4yhk]], [[Resolution\|resolution]] 2.21Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[4yhk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4YHK OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4YHK FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=4CC:N-[(2-{[(4-CARBAMIMIDOYLPHENYL)AMINO]METHYL}-1-METHYL-1H-BENZIMIDAZOL-5-YL)CARBONYL]-N-PYRIDIN-2-YL-BETA-ALANINE'>4CC</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4yhk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4yhk OCA], [http://pdbe.org/4yhk PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=4yhk RCSB], [http://www.ebi.ac.uk/pdbsum/4yhk PDBsum]</span></td></tr>
		+	</table>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Novel oral anticoagulants are effective and safe alternatives to vitamin-K antagonists for anticoagulation therapy. However, anticoagulation therapy in general is associated with an elevated risk of bleeding. Idarucizumab is a reversal agent for the direct thrombin inhibitor, dabigatran etexilate (Pradaxa(R)) and is currently in Phase 3 studies. Here, we report data on the antibody fragment aDabi-Fab2, a putative backup molecule for idarucizumab. Although aDabi-Fab2 completely reversed effects of dabigatran in a rat model in vivo, we observed significantly reduced duration of action compared to idarucizumab. Rational protein engineering, based on the X-ray structure of aDabi-Fab2, led to the identification of mutant Y103W. The mutant had optimized shape complementarity to dabigatran while maintaining an energetically favored hydrogen bond. It displayed increased affinity for dabigatran, mainly driven by a slower off-rate. Interestingly, the increased residence time translated into longer duration of action in vivo. It was thus possible to further enhance the efficacy of aDabi-Fab2 based on rational design, giving it the potential to serve as a back-up candidate for idarucizumab.

-	~~The entry 4yhk is ON HOLD until Paper Publication~~	+	Structure-guided residence time optimization of a dabigatran reversal agent.,Schiele F, van Ryn J, Litzenburger T, Ritter M, Seeliger D, Nar H MAbs. 2015 Jun 5:0. PMID:26047352<ref>PMID:26047352</ref>

-	~~Authors: Schiele~~, F.~~, Nar, H~~.	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-		+	</div>
-	~~Description~~: ~~Reversal Agent for Dabigatran~~	+	<div class="pdbe-citations 4yhk" style="background-color:#fffaf0;"></div>
-	~~[[Category: Unreleased Structures]]~~	+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
	[[Category: Nar, H]]		[[Category: Nar, H]]
	[[Category: Schiele, F]]		[[Category: Schiele, F]]
		+	[[Category: Antibody]]
		+	[[Category: Antidote]]
		+	[[Category: Dabigatran]]
		+	[[Category: Immune system]]
		+	[[Category: Pradaxa]]
		+	[[Category: Reversal agent]]

OCA: Protected "4yhk" [edit=sysop:move=sysop]

OCA — Wed, 11 Mar 2015 10:37:39 GMT

Protected "4yhk" [edit=sysop:move=sysop]

←Older revision

Revision as of 10:37, 11 March 2015

OCA: New page: '''Unreleased structure''' The entry 4yhk is ON HOLD until Paper Publication Authors: Schiele, F., Nar, H. Description: Reversal Agent for Dabigatran [[Category: Unreleased Structures]...

OCA — Wed, 11 Mar 2015 10:37:37 GMT

New page: '''Unreleased structure''' The entry 4yhk is ON HOLD until Paper Publication Authors: Schiele, F., Nar, H. Description: Reversal Agent for Dabigatran [[Category: Unreleased Structures]...

New page

'''Unreleased structure'''

The entry 4yhk is ON HOLD until Paper Publication

Authors: Schiele, F., Nar, H.

Description: Reversal Agent for Dabigatran
[[Category: Unreleased Structures]]
[[Category: Nar, H]]
[[Category: Schiele, F]]